2GV2

MDM2 in complex with an 8-mer p53 peptide analogue

• PDB DOI: https://doi.org/10.2210/pdb2GV2/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-02 Released: 2006-09-05 
• Deposition Author(s): Schubert, C., Sakurai, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Crystallographic Analysis of an 8-mer p53 Peptide Analogue Complexed with MDM2.

Sakurai, K., Schubert, C., Kahne, D.

(2006) J Am Chem Soc 128: 11000-11001

• PubMed: 16925398 
• DOI: https://doi.org/10.1021/ja063102j
• Primary Citation of Related Structures:  
  2GV2


• PubMed Abstract: 
  

  The most potent inhibitor of the p53-MDM2 interaction reported to date is an 8-mer p53 peptide analogue (Novartis peptide), which contains 6-chlorotryptophane (Cl-Trp) and phosphonomethylphenylalanine (Pmp) as key residues for the enhanced activity. We report here a crystal structure of the co-complex between MDM2 and the Novartis peptide solved at 1.8 A resolution. The structural basis for the role of the two aromatic residues are delineated by comparing the present structure with crystal structures of the MDM2 co-complex bound to other inhibitors including the wt-p53 peptide itself.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.79 kDa 
• Atom Count: 923 
• Modelled Residue Count: 97 
• Deposited Residue Count: 119 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	110	Homo sapiens	Mutation(s): 0  Gene Names: MDM2 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
PHAROS:  Q00987 GTEx:  ENSG00000135679

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
8-MER P53 PEPTIDE ANALOGUE	B	9	N/A	Mutation(s): 0

Small Molecules

Modified Residues  4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
1AC	B	PEPTIDE LINKING	C4 H7 N O2		ALA
6CW	B	L-PEPTIDE LINKING	C11 H11 Cl N2 O2		TRP
AIB	B	L-PEPTIDE LINKING	C4 H9 N O2		ALA
PM3	B	L-PEPTIDE LINKING	C10 H14 N O5 P		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.66	α = 90
b = 44.1	β = 90
c = 59.15	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
ADSC	data collection
HKL-2000	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-05 
Deposition Author(s): Schubert, C., Sakurai, K.

Revision History  

• Version 1.0: 2006-09-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 1.4: 2023-11-15
  Changes: Data collection